Again, there is a problem of what exactly is ID. ID advocates have
been saying that "junk DNA" isn't junk. However, whether or not one
expects there to be junk DNA would require certain assumptions about
the methods and intent of the designer. Thus ID has no a priori
reason to not expect junk DNA nor to expect it, and complaints about
scientific vacuity have some merit. On the other hand, ID opponents
have invoked junk DNA as something not expected from ID. This of
course makes assumptions (also frequently made by ID advocates) about
what a designer ought to do.

The results pose problems for other ID claims. The fact that certain
functional sequences can vary drastically is problematic for the
claims of low probability of obtaining a functional sequence that
underlie specified complexity or irreducible complexity arguments.

The pattern in which such sequences vary agrees with the expectations
of common descent (with caveats about paralogy, differential loss of
ancestral polymorphism, hybridization, etc.), something denied by many
popular versions of ID. For example, ITS1 and 2 are apparently
functionally important in spacing the ribosomal RNA genes, but their
sequences are free to vary greatly. Things expected evolutionarily to
be closely related have more similar sequences.

Evolution is expected to place some pressure towards weeding out of
unneeded DNA (how much pressure varying greatly depending on the
organism's lifestyle and environment), so a limited amount of truly
useless DNA would be expected evolutionarily. The fact that much DNA
previously not known to have function does have a function is thus not
a good argument against evolution nor for design, just as the presence
of a bunch of totally unused DNA does not in itself argue for
evolution nor against design. (Evolution and design of course ought
not to be considered mutually exclusive, contrary to a major chunk of
the bad theology underlying creation-evolution arguments.)
Examination of the sequences themselves and their apparent
relationships argues for evolution and against separate creation of
either organisms or genetic diversity.

--
Dr. David Campbell
425 Scientific Collections
University of Alabama
"I think of my happy condition, surrounded by acres of clams"
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